find motif locations in the genome

Question

[igor]

There are many motif-finding tools. Usually they compare a set of sequences against a set of motifs and give you the top occurring motifs. However, I have a specific motif in mind and I would like to find the positions where it occurs in the genome (account for mismatches, of course). Is there a tool that will do that?

Answer 1

[GenoMax]

Recent thread that may work: Finding specific k-mer in human genome

[igor]

Doesn't k-mer imply that the sequence has to be an exact match?

[GenoMax]

fuzznuc, EMBOSS program referenced in the thread allows you to specify search patterns (with mismatches): http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html I assume you know the sequence of the motif you want to search. You can specify search patterns based on that.

Answer 2

[Alex Reynolds]

The command-line version of UCSC BLAT can be used locally with -minMatch and -minIdentity options to account for mismatches. It exports a PSL file, which contains position information and can be converted into other formats for operations.

[gangireddy]

I think blast also should work, doesn't it?

If not what might be the possible problems

[Alex Reynolds]

I think BLAT will give you a bit more control over the number of allowed mismatches and other settings. It also directly outputs positional information, which I do not believe blast does without extra work.

[igor]

I think BLAT needs a lot more modifications. Setting -minIdentity=60 and -minMatch=1 fails to match a 20bp sequence with just 1 mismatch.